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Billerbeck, S.

Publications and source records attributed to Billerbeck, S..

7 recordsLinked to original sources

A co-evolved peptide-GPCR system senses host entry to drive fungal infection

A successful infection requires pathogens to recognize the specific host environment in order to reprogram their physiology accordingly. One major way in which eukaryotic cells sense their surroundings is via G-Protein Coupled Receptors (GPCRs), which share a seven-transmembrane architecture and G-protein-mediated downstream signaling. While mammalian GPCRs are well-characterized and represent important drug targets, their fungal counterparts remain poorly understood. In the corn pathogen Ustilago maydis, we now uncover a GPCR-based mechanism that allows the fungus to scout the host environment to sense whether it has entered into the plant tissue. During infection, the fungus secretes the protein Pit2, which is cleaved by host apoplastic-cysteine proteases, releasing a peptide ligand hidden within Pit2. This ligand activates the fungal GPCR Gpe1 strongly promoting fungal proliferation after initial host penetration. Comparative analyses reveal conservation of the Gpe1/Pit2 system, with co-evolutionary signatures preserving receptor-ligand specificity. Furthermore, this GPCR system recognizing hidden peptide ligands shows conceptual similarities to the fungal pheromone mating system, without sharing sequence similarity. Our findings reveal a co-evolved mechanism between fungus and host that encodes environmental context into a protein scaffold, establishing a novel paradigm for host-dependent signaling with implications for inter-organismic communication.

microbiology↗

Unveiling the Molecular Architecture of Candida auris Ribosome

Candida auris is an emerging multidrug-resistant fungal pathogen causing life-threatening invasive candidiasis and bloodstream infections (candidemia), posing significant global health challenges. Despite its importance, the protein translation in pathogenic fungi is poorly characterized. Using cryo-electron microscopy and single-particle reconstruction, we resolved high-resolution structures of the 80S ribosome from C. auris in its vacant state and in complexes with three inhibitors: cycloheximide (CHX), blasticidin-S (BLS), and geneticin (G418). We uncovered a unique substitution of a key nucleotide in the P-site of the small ribosomal subunit (C1160 in C. auris), which may influence ribosome-tRNA interactions and translation fidelity. Comparative analysis of ribosome inhibitor interactions showed that resistance to CHX was observed in only two Candida species examined, while BLS binding displayed no significant differences between C. auris and S. cerevisiae, although C. auris was more sensitive to it. We identified that G418 exhibits promiscuous binding across multiple nonspecific sites, yet its primary interaction site at the decoding center remains highly conserved among Candida species. These findings provide a previously uncharacterized structure of the C. auris ribosome, highlighting novel features that may be leveraged for the development of targeted antifungal therapies to combat multidrug resistance. These insights not only enhance our understanding of ribosomal inhibitor interactions but also suggest potential biomarkers for predicting antifungal susceptibility in clinical applications.

molecular biology↗

Pulcherriminic acid biosynthesis and Transport: Insights from a heterologous system in Saccharomyces cerevisiae

Pulcherriminic acid is an iron chelator produced by some Kluyveromyces and Metschnikowia yeasts. Its biosynthesis is encoded by the four-gene PUL cluster, where PUL1 and PUL2 are the biosynthetic enzymes, PUL3 mediates the uptake of iron-bound pulcherrimin, and PUL4 is a putative regulator. Pulcherriminic acid holds antifungal potential, as the growth of organisms unable to uptake pulcherrimin is inhibited by deficit of essential iron. Thus, a heterologous production system to further characterize and optimize its biosynthesis would be valuable. Using our in-house yeast collection and genomes available in databases, we cloned PUL1 and PUL2 genes from K. lactis and one of our wild Metschnikowia isolates and built an effective production system in S. cerevisiae able to inhibit pathogenic growth. In this context, the K. lactis genes yielded faster pulcherriminic acid production than those from the Metschnikowia isolate and a combinatorial approach showed PUL1 to be the production bottleneck. We further showed that Pul3 is an importer of pulcherrimin, but also mediates the export of pulcherriminic acid and that the growth of pathogens like Candidozyma auris and organisms encoding PUL3 in their genome, previously called "cheaters", is inhibited by pulcherriminic acid, highlighting its potential as an antimicrobial agent.

microbiology↗

Alanine-scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure.

Yeast killer toxins (YKTs) are antimicrobial proteins secreted by yeast with potential applications ranging from food preservation to therapeutic agents in human health. However, the practical use of many YTKs is limited by specific pH requirements, low temperature stability, low production yields, and narrow target specificity. While protein engineering could potentially overcome these challenges, progress is hindered by a lack of detailed knowledge about sequence-function relationships and structural data for these often multi-step processed proteins. In this study, we focused on the YKT K2, encoded by the M2 dsRNA satellite virus in Saccharomyces cerevisiae. Using alanine scanning mutagenesis of the full open reading frame and structure predictions combined with molecular dynamics simulations, we generated a comprehensive sequence-function map, refined the model for the proteolytic processing of the K2 precursor, and predicted the mature toxin structure. Our findings also demonstrate that K2 can be engineered towards enhanced toxicity and altered target specificity through single-site mutations. Furthermore, we identified structural homology between K2 and the SMK toxin from the yeast Millerozyma farinosa. Our cost-effective workflow provides a platform to broadly map YKT sequence-structure-function relationships, facilitating the engineering towards toxin-based technologies. The workflow could also serve as a template to resolve the processing and conformations of other proteins within the secretory pathway - a dynamic multi-step process that is challenging to structurally capture by purification and solving structures of intermediates.

microbiology↗

The antifungal capacity of an 681-membered collection of environmental yeast isolates

Fungal pathogens threaten human health and food security, with resistance reported across limited antifungal classes. Novel strategies to control these pathogens and food spoilers are urgently needed. Environmental yeasts provide a functionally diverse, yet underexploited potential for fungal control based on their natural competition via the secretion of iron siderophores, killer toxins (proteins) or other small molecules like volatile organic compounds or biosurfactants. However, there is a lack of standardized workflows to systematically access application- relevant yeast-based compounds and understand their molecular functioning. Towards this goal, we developed a workflow to identify and characterize yeast isolates that are active against relevant human and plant pathogens and spoilage yeasts, herein focusing on discovering yeasts that produce potential killer toxins. The workflow includes the classification of the secreted molecules and cross-comparison of their antifungal capacity using an independent calibrant. Our workflow delivered a collection of 681 yeasts of which 212 isolates (31%) displayed antagonism against at least one of our target strains. While 50% of the active yeasts showed iron-depended antagonism, likely due to siderophore production, more than 25% are potentially secreting a toxic protein. Those killer yeast candidates clustered within ten species, showed target profiles from narrow- to broad spectrum, and several showed a broad pH and temperature activity profile. Given the tools for yeast biotechnology and protein engineering available, our collection offers a foundation for genetic and molecular characterization of antifungal phenotypes, with potential for future exploitation. The scalable workflow can screen other yeast collections or adjust for different antifungal compounds.

microbiology↗

The signal sequence of yeast killer toxin K2 confers producer self-protection and allows conversion into a modular toxin-antitoxin system

Some antimicrobial proteins secreted by yeast, known as yeast killer toxins, also target the producer species itself, necessitating a means of self-protection. Intriguingly, the M2 dsRNA killer virus in Saccharomyces cerevisiae contains a single open reading frame (ORF) that encodes both the pore-forming killer toxin K2 as well as a cognate immunity factor. Here, a systematic deletion screen reveals that expression of a 49-amino acid N-terminal peptide from this ORF is both necessary and sufficient for immunity and that the K2 toxin and this 49-residue immunity peptide can be functionally split into a modular toxin-antitoxin system. Further, the immunity peptide exhibits characteristics of a signal peptide and we thus propose that the K2 signal peptide serves a dual function: 1) Toxin targeting into the secretory pathway, and 2) establishing self-protective immunity. This case further implies that (signal) peptides form a potential source for antimicrobial resistance.

microbiology↗

A modular cloning toolbox including CRISPRi for the engineering of the human fungal pathogen and biotechnology host Candida glabrata

The yeast Candida glabrata is an emerging, often drug-resistant opportunistic human pathogen, that can cause severe systemic infections in immunocompromised individuals. At the same time, it is a valuable biotechnology host that naturally accumulates high levels of pyruvate - a valuable chemical precursor. Tools for the facile engineering of this yeast could greatly accelerate studies on its pathogenicity and its optimization for biotechnology. While a few tools for plasmid-based expression and CRISPR/Cas-based genome engineering have been developed, there is no well-characterized cloning toolkit available that would allow the assembly of pathways or genetic circuits in a modular fashion. Here, by re-using and characterizing the Saccharomyces cerevisiae-based yeast molecular cloning toolkit (YTK) in C. glabrata and by adding missing components, we build a well-characterized CgTK (Candida glabrata toolkit). We used the CgTK to build a CRISPR interference system for C. glabrata that can be used to generate selectable phenotypes via single-gRNA targeting such as required for genome-wide library screens.

microbiology↗